tblastn_options.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: tblastn_options.hpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 18:03:12  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
 * PRODUCTION
 * ===========================================================================
 */

#ifndef ALGO_BLAST_API___TBLASTN_OPTIONS__HPP
#define ALGO_BLAST_API___TBLASTN_OPTIONS__HPP

/*  $Id: tblastn_options.hpp,v 1000.2 2004/06/01 18:03:12 gouriano Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Authors:  Christiam Camacho
 *
 */

/// @file tblastn_options.hpp
/// Declares the CTBlastnOptionsHandle class.

#include <algo/blast/api/blast_prot_options.hpp>

/** @addtogroup AlgoBlast
 *
 * @{
 */

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)

/// Handle to the protein-translated nucleotide options to the BLAST algorithm.
///
/// Adapter class for protein-translated nucleotide BLAST comparisons.
/// Exposes an interface to allow manipulation the options that are relevant to
/// this type of search.

class NCBI_XBLAST_EXPORT CTBlastnOptionsHandle : 
                                            public CBlastProteinOptionsHandle
{
public:

    /// Creates object with default options set
    CTBlastnOptionsHandle(EAPILocality locality = CBlastOptions::eLocal);
    ~CTBlastnOptionsHandle() {}

    /************************ Scoring options ************************/
    // is this needed or can we use a sentinel for the frame shift penalty?
    bool GetOutOfFrameMode() const { return m_Opts->GetOutOfFrameMode(); }
    void SetOutOfFrameMode(bool m = true) { m_Opts->SetOutOfFrameMode(m); }

    int GetFrameShiftPenalty() const { return m_Opts->GetFrameShiftPenalty(); }
    void SetFrameShiftPenalty(int p) { m_Opts->SetFrameShiftPenalty(p); }

    int GetLongestIntronLength() const { return m_Opts->GetLongestIntronLength(); }
    void SetLongestIntronLength(int l) { m_Opts->SetLongestIntronLength(l); }

    /******************* Subject sequence options *******************/
    int GetDbGeneticCode() const {
        return m_Opts->GetDbGeneticCode();
    }
    void SetDbGeneticCode(int gc) {
        m_Opts->SetDbGeneticCode(gc);
    }

protected:
    void SetLookupTableDefaults();
    void SetScoringOptionsDefaults();
    void SetHitSavingOptionsDefaults();
    void SetSubjectSequenceOptionsDefaults();

private:
    CTBlastnOptionsHandle(const CTBlastnOptionsHandle& rhs);
    CTBlastnOptionsHandle& operator=(const CTBlastnOptionsHandle& rhs);
};

END_SCOPE(blast)
END_NCBI_SCOPE


/* @} */


/*
 * ===========================================================================
 * $Log: tblastn_options.hpp,v $
 * Revision 1000.2  2004/06/01 18:03:12  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
 *
 * Revision 1.8  2004/05/04 13:09:20  camacho
 * Made copy-ctor & assignment operator private
 *
 * Revision 1.7  2004/03/19 14:53:24  camacho
 * Move to doxygen group AlgoBlast
 *
 * Revision 1.6  2004/01/20 15:19:25  camacho
 * Provide missing default parameters to default ctor
 *
 * Revision 1.5  2004/01/16 20:42:57  bealer
 * - Add locality flag for blast options handle classes.
 *
 * Revision 1.4  2003/12/15 18:42:06  dondosha
 * Added longest intron length setter/getter
 *
 * Revision 1.3  2003/12/09 12:40:23  camacho
 * Added windows export specifiers
 *
 * Revision 1.2  2003/12/03 16:34:58  dondosha
 * SetDbGeneticCode now fills both integer and string option
 *
 * Revision 1.1  2003/11/26 18:22:18  camacho
 * +Blast Option Handle classes
 *
 * ===========================================================================
 */

#endif  /* ALGO_BLAST_API___TBLASTN_OPTIONS__HPP */